Article 35.

Genomic differentiation of three pico-phytoplankton species in the Mediterranean Sea. 2022. Environmental Microbiology, in press

Authors: Da Silva, […], Leconte J, […], Bittner L.

https://doi.org/10.1111/1462-2920.16171

 

• Metagenomics offers new opportunities to study of genetic differentiation
• Both distance and environment could drive protists’ genetic differentiation
• Such approach is limited to abundant species with reference assembly
• So far the main limit remains the low sequencing coverages

Article 34.

Towards omics-based predictions of planktonic functional composition from environmental data. 2021. Nature communications 12:4361.

Authors: Faure E, Ayata SD, Bittner L.

Article 33.

Functional trait-based approaches as a common framework for aquatic ecologists. 2021. Limnology and Oceanography 66: 965–994.

Authors: Martini S,  […] Faure E, […], Bittner L, […], Ayata SD

Article 32.

A resource-frugal probabilistic dictionary and applications in bioinformatics. 2020. Discrete Applied Mathematics 274:90-102.

Authors: Marchet C, Lecompte L, Limasset A, Bittner L, Peterlongo P.

https://doi.org/10.1016/j.dam.2018.03.035

Article 31.

Community‐Level Responses to Iron Availability in Open Ocean Planktonic Ecosystems. 2019. Global Biogeochemical Cycles 33(3): 391-419.

 

Article 30.

Mixotrophic protists display contrasted biogeographies in the global ocean. 2019. The ISME Journal Jan 14, 13:1072-1083.

 

29. Lewitus E, Bittner L, Malviya S, Bowler C, Morlon H. 2018 Clade-specific diversification dynamics of marine diatoms since the Jurassic. Nature Ecology & Evolution 2018 Nov;2(11):1715-1723.

https://doi.org/10.1038/s41559-018-0691-3

28. Meng A, Marchet C, Corre E, Peterlongo P, Alberti A, Da Silva C, Wincker P, Pelletier E, Probert I, Decelle J, Le Crom S, Not F, Bittner L. 2018 A de novo approach to disentangle partner identity and function in holobiont system. Microbiome 2018 Jun 9;6(1):105.

https://doi.org/10.1186/s40168-018-0481-9

27. Meng A, Corre E, Probert I, Gutierrez-Rodriguez A, Siano R, Annamale A, Alberti A, Da Silva C, Wincker P, Le Crom S, Not F(*), Bittner L(*) (* last co-authors). 2018 Analysis of the genomic basis of functional diversity in dinoflagellates using a transcriptome-based sequence similarity network. Molecular Ecology 27(10):2365-2380

https://doi.org/10.1111/mec.14579

26. Vincent F, Colin S, Romac S, Scalco E, Bittner L, Dolan JR, Zingone A, de Vargas C, Bowler C. 2018 The epibiotic life of the cosmopolitan diatom Fragilariopsis doliolus on heterotrophic ciliates in the open ocean. The ISME Journal 2018 Apr;12(4):1094-1108.

https://doi.org/10.1038/s41396-017-0029-1

25. Tréguer P, Bowler C, Moriceau B, Dutkiewicz S, Gehlen M, Aumont O, Bittner L, Dugdale R, Finkel Z, Iudicone D, Jahn O, Guidi L, Lasbleiz M, Leblanc K, Levy M, Pondaven P. 2018 Diatoms: role in biological carbon pump of present and future oceans. Nature Geoscience 11, pp. 27–37 [review article]

https://doi.org/10.1038/s41561-017-0028-x

24. Benoiston AS *, Ibarbalz FM* (* first co-authors), Bittner L, Guidi L, Jahn O, ,Dutkiewicz S, Bowler C, 2017. The evolution of diatoms and their biogeochemical functions. Philosophical Transactions of the Royal Society B. [review article]

https://doi.org/10.1098/rstb.2016.0397

23. Botebol H, Lelandais G, Six C, Lesuisse E, Meng A, Bittner L, Le Crom S, Sutak R, Lozano JC, Schatt P, Vergé V, Blain S, Bouget FY, 2017. Acclimation of a low iron adapted Ostreococcus strain to iron limitation through cell biomass reduction Scientific Reports Mar 23;7(1):327.

https://doi.org/10.1038/s41598-017-00216-6

22. Chust G, Vogt M, Benedetti F, Nakov T, Villéger S, Aubert A, Vallina SM, Righetti D, Not F, Biard T, Bittner L, Benoiston AS, Guidi L, Villarino E, Gaborit C, Cornils A, Buttay L, Irisson JO, Chiarello M, Vallim Lima A, Blanco-Bercial L, Basconi L, Ayata SD, 2017. Mare incognitum: A glimpse into future plankton diversity and ecology. Frontiers in Marine Science, section Marine Ecosystem Ecology Article type: Mini Review. [review article]

https://doi.org/10.3389/fmars.2017.00068

21. Forster D, Dunthorn M, Mahé F, Dolan JR, Audic S, Bass D, Bittner L, Boutte C, Christen R, Claverie JM, Decelle J, Edvardsen B, Egge E, Eikrem W, Gobet A, Kooistra WH, Logares R, Massana R, Montresor M, Not F, Ogata H, Pawlowski J, Pernice MC, Romac S, Shalchian-Tabrizi K, Simon N, Richards TA, Santini S, Sarno D, Siano R, Vaulot D, Wincker P, Zingone A, de Vargas C, Stoeck T, 2016. Benthic protists: the under-charted majority, FEMS Microbiology Ecology 2016 Aug;92(8). pii: fiw120. Epub 2016 Jun 5.

https://doi.org/10.1093/femsec/fiw120

20. Malviya S, Scalco E, Audic S, Vincent F, Veluchamy A, Poulain J, Wincker P, Iudicone D, De Vargas C, Bittner L, Zingone A, Bowler C, 2016. Insights into global diatom distribution and diversity in the world’s ocean. Proceedings of the National Academy of Sciences, published ahead of print February 29, 2016.

https://doi.org/10.1073/pnas.1509523113

19. Guidi L*, Chaffron S*, Bittner L*, Eveillard D* (* first co-authors), Larhlimi A, Roux S, Darzi Y, Audic S, Berline L, Brum J, Coelho LP, Espinoza JCI, Malviya S, Sunagawa S, Dimier C, Kandels-Lewis S, Picheral M, Poulain J, Searson S, Tara Oceans coordinators, Stemmann L, Not F, Hingamp P, Speich S, Follows M, Karp-Boss L, Boss E, Ogata H, Pesant S, Weissenbach J, Wincker P, Acinas SG, Bork P, de Vargas C, Iudicone D, Sullivan MB, Raes J, Karsenti E, Bowler C, Gorsky G, 2016. Plankton networks driving carbon export in the oligotrophic ocean. Nature, 2016 Feb 10.

https://doi.org/10.1038/nature16942

18. Massana R, Gobet A, Audic S, Bass D, Bittner L, Boutte C, Chambouvet A, Christen R, Claverie JM, Decelle J, Dolan J , Dunthorn M, Edvardsen B, Forn I, Forster D, Gouillou L, Jaillon O, Kooistra WHCF, Logares R, Mahé F, Not F, Ogata H, Pawlowski J, Pernice MC, Probert I, Romac S, Richards T, Santini S, Shalchian-Tabrizi K, Siano R, Simon N, Stoeck T, Vaulot D, Zingone A, de Vargas C, 2015. Marine protist diversity in European coastal waters and sediments as revealed by high-throughput sequencing. Environmental Microbiology, 17(10): 4035-4049.

https://doi.org/10.1111/1462-2920.12955

17. Lima-Mendez G*, Faust K*, Henry N* (* first co-authors), Decelle J, Colin S, Carcillo F, Chaffron S, Ignacio-Espinosa JC, Vincent F, Bittner L, Darzi Y, Wang J, Audic S, Berline L, Bontempi G, Copola L, Cornejo-Castillo FM, d’Ovidio F, Demeester L, Garet-Delmas MJ, Guidi L, Pesant S, Salazar G, Dimier C, Picheral M, Searson S, Kandel-Lewis S, Tara Oceans coordinators, Acinas SG, Gorsky G, Not F, Ogata H, Speich S, Weissenback J, Wincker P, Sunagawa S, Bork P, Sullivan M, Bowler C, Karsenti E, de Vargas C, Raes J, 2015. Top-down determinants of community structure in the global plankton interactome. Science, 348(6237):1262073.

https://doi.org/10.1126/science.1262073

16. de Vargas C*, Audic S*, Henry N*, Decelle J*, Mahé F* (*first co-authors), Logares R, Lara E, Berney C, Le Bescot N, Probert I, Carmichael M, Poulain J, Romac S, Colin S, Aury JM, Bittner L, Chaffron S, Dunthorn M, Engelen S, Flegontova O, Guidi L, Horak A, Jaillon O, Lima-Mendez G, Lukes J, Malviya S, Morard R, Mulot M, Scalco E, Siano R, Vincent F, Zingone A, Dimier C, Picheral M, Searson S, Kandel-Lewis S, Tara Oceans coordinators, Acinas SG, Bork P, Bowler C, Gorsky G, Grimsley N, Hingamp P, Iudicone D, Not F, Ogata H, Pesant S, Raes J, Sieracki ME, Speich S, Stemman L, Sunagawa S, Weissenbach J, Wincker P, Karsenti E, 2015. Eukaryotic plankton diversity in the sunlit ocean. Science, 348(6237):1261605.

https://doi.org/10.1126/science.1261605

15. Villar E, Farrant GK, Follows M, Garczarek L, Speich S, Audic S, Bittner L, Blanke B, Brum JR, Brunet C, Casotti R, Chase A, Dolan JR, d’Ortenzio F, Gattuso JP, Grima N, Guidi L, Hill CN, Jahn O, Jamet J-L, Le Goff H, Lepoivre C, Malviya S, Pelletier E, Romagnan JB, Roux S, Santini S, Scalco E, Schwenck SM, Tanaka A, Testor P, Vannier T, Vincent F, Zingone A, Dimier C, Picheral M, Searson S, Kandels-Lewis S, Tara Oceans coordinators, Acinas SG, Bork P, Boss E, Bowler C, Vargas C de, Gorsky G, Ogata H, Pesant S, Sullivan MB, Sunagawa S, Wincker P, Karsenti E, Bowler C, Not F*, Hingamp P*, Iudicone D* (*co-senior authors), 2015. Environmental characteristics of Agulhas rings affect inter-ocean plankton transport. Science, 48(6237):1261447.

https://doi.org/10.1126/science.1261447

14. Egge ES, Johannessen TV, Andersen T, Eikrem W, Bittner L, Larsen A, Sandaa RA, Edvardsen B, 2015. Seasonal dynamics of haptophytes in the Skagerrak, Norway, explored by high-throughput sequencing. Molecular Ecology, 24: 3026–3042.

https://doi.org/10.1111/mec.13160

13. Forster D*, Bittner L* (* first co-authors), Karkar S, Dunthorn M, Romac S, Audic S, Lopez P, Stoeck T* & Bapteste E* (*co-senior authors), 2015. Testing ecological theories with sequence similarity networks: marine ciliates exhibit similar geographic dispersal patterns as multicellular organisms. BMC Biology, 13:16.

https://doi.org/10.1186/s12915-015-0125-5

12. Logares R, Audic S, Bass D, Bittner L, Boutte C, Christen R, Claverie JM, Decelle J, Dolan JR, Dunthorn M, Edvardsen B, Gobet A, Kooistra WHCF, Mahé F, Not F, Ogata H, Pawlowski J, Pernice MC, Romac S, Shalchian-Tabrizi K, Simon N, Stoeck T, Santini S, Siano R, Wincker P, Zingone A, Richards TA, de Vargas C, Massana R, 2014. Patterns of rare and abundant marine microbial eukaryotes. Current Biology, 24(8):813–821.

https://doi.org/10.1016/j.cub.2014.02.050

11. Egge ES, Bittner L, Andersen T, Audic S, de Vargas C, Edvardsen B, 2013. 454-pyrosequencing to describe microbial eukaryotic community composition, diversity and relative abundance: a test for marine Haptophytes. PLoS ONE, 8(9): e74371.

https://doi.org/10.1371/journal.pone.0074371

10. Silberfeld T, Bittner L, Fernández-García C, Cruaud C, Reviers B de, Rousseau F, Leliaert F, Payri CE, De Clerck O, 2013. Species diversity, phylogeny and large scale biogeographical patterns of the genus Padina (Phaeophyceae, Dictyotales). Journal of Phycology, 49,130-142.

https://doi.org/10.1111/jpy.12027

9. Bittner L, Gobet A, Audic S, Romac S, Egge ES, Santini S, Ogata H, Probert I, Edvardsen B, de Vargas C, 2013. Diversity patterns of uncultured Haptophytes unravelled by pyrosequencing in Naples Bay. Molecular Ecology, 22(1): 87-101.

https://doi.org/10.1111/mec.12108

8. Guillou L, Dipankar B, Audic S, Bass D, Berney C, Bittner L, Boutte C, Burgaud G, de Vargas C, Decelle J, del Campo J, Dolan J, Dunthorn M, Edvardsen B, Holzmann M, Kooistra W, Lara E, Le Bescot N, Logares R, Mahé F, Massana R, Montresor M, Morard R, Not F, Pawlowski J, Probert I, Sauvadet A-L, Siano R, Stoeck T, Vaulot D, Zimmermann P, Christen R, 2013. The Protist Ribosomal Reference database (PR2): a catalog of unicellular eukaryote Small SubUnit rRNA sequences with curated taxonomy. Nucleic Acids Research, 41(D1): D597-D604.

https://doi.org/10.1093/nar/gks1160

7. Sperling M, Piontek J, Gerdts G, Wichels A, Schunck H, Roy A-S, La Roche J, Gilbert J, Nissimov J, Bittner L, Romac S, Riebesell U, Engel A, 2013. Effect of elevated CO2 on the dynamics of particle attached and free living bacterioplankton communities in an Arctic fjord. Biogeoscience, 10: 181-191.

https://doi.org/10.5194/bg-10-181-2013

6. Roy A-S, Gibbons SM, Schunck H, Owens S, Caporaso JG, Sperling M, Nissimov J, Romac S, Bittner L, Riebesell U, La Roche J, Gilbert JA, 2013. Ocean acidification shows negligible impacts on high-latitude bacterial community structure in coastal pelagic mesocosms. Biogeoscience, 10: 555-566-191.

https://doi.org/10.5194/bg-10-555-2013

5. Decelle J, Probert I, Bittner L, Desdevises Y, Colin S, De Vargas C, Gali M, Simó R, Not F, 2012. An original mode of symbiosis in open ocean plankton. Proceedings of the National Academy of Sciences, 109(44): 18000-18005.

https://doi.org/10.1073/pnas.1212303109

4. Bittner L, Payri CE, Maneveldt GW, Couloux A, Cruaud C, de Reviers B, Le Gall L, 2011. Evolutionary history of the Corallinales (Corallinophycidae, Rhodophyta) inferred from nuclear, plastidial and mitochondrial genomes. Molecular phylogenetics and evolution, 61, 3:697-713. 

https://doi.org/10.1016/j.ympev.2011.07.019

3. Bittner L *, Halary S* (* first co-authors), Payri CE, Cruaud C, de Reviers B, Lopez P, Bapteste E, 2010. Some considerations for analyzing biodiversity using integrative metagenomics and gene networks. Biology Direct, 5:47.

https://doi.org/10.1186/1745-6150-5-47

2. Le Gall L, Payri CE, Bittner L, Saunders GW, 2010. Multigene phylogenetic analyses support recognition of the Sporolithales ord. nov. Molecular phylogenetics and evolution., 54, 1:302-305.

https://doi.org/10.1016/j.ympev.2009.05.026

1. Bittner L, Payri CE, Couloux A, Cruaud C, De Reviers B, Rousseau F, 2008. Molecular phylogeny of the Dictyotales and their position within the Phaeophyceae, based on nuclear, plastid and mitochondrial DNA sequence data. Molecular phylogenetics and evolution 49 (1), 211-226.

https://doi.org/10.1016/j.ympev.2008.06.018